Hydroperoxides of 18:2n-6 and 20:4n-6 were obtained by autoxidation and photooxidation. The enantiomers were separated as free acids (Reprosil Chiral-NR column, eluted with hexane containing 1-1.2% alcoholic modifier) and analyzed by on line UV detection (234 nm) and liquid chromatography-MS/MS/MS of carboxylate anions (A(-)-->(A(-)-18)-->full scan) in an ion trap. The combination of UV and MS/MS/MS analysis facilitated identification of hydroperoxides even in complex mixtures of autoxidized or photooxidized fatty acids. The signal intensities increased about two orders of magnitude by raising the isolation width of A(-) from 1.5 amu to 5 or 10 amu for cis-trans conjugated hydroperoxy fatty acids, and one order of magnitude or more for non-conjugated hydroperoxy fatty acids. The S enantiomer of 8-, 9-, 10-, and 13-hydroperoxyoctadecadienoic acids and the S enantiomer of cis-trans conjugated hydroperoxyeicosatetraenoic acids eluted before the corresponding R enantiomer with two exceptions (11-hydroperoxylinoleic acid and 8-hydroperoxyeicosa-5Z,9E,11Z,14Z-tetraenoic acid). The separation of enantiomers or regioisomers could be improved by the choice of either isopropanol or methanol as alcoholic modifier.